In practice, precision nutrition in aquaculture is envisioned to provide all essential nutrients to the fish as accurately as possible by using locally available sustainable feedstuffs, subject to the species, development phase, and culture conditions to ensure sustainability. In the aquafeed industry, due to lower prices, wide availability, and good nutritional profile, using alternative protein and energy sources of plant origin compared to animal origin is gaining popularity. This is a sustainable approach, although the inappropriate use of plant sources in aquafeed may have a negative impact on the nutritional quality of fish. We delve into and summarize the epigenetic regulation of energy metabolism in fish to enhance the feed utilization efficiency of animals in response to aquafeed containing plant sources. Unlike the genome, which is largely static, the epigenome is much dynamic and shows differences across cell types. Epigenetic alterations are critical for various important biological processes, such as cellular differentiation, genomic imprinting, and X-chromosome inactivation. This finding could be greatly valuable for researchers working on aquaculture nutrition and physiology to help aquaculturists execute effective and sustainable nutritional strategies to ensure sustainable aquaculture in the long run.